Simulation Foundries
OverviewProgramme: This Project is not associated with a Programme
SEEK ID: https://fairdomhub.org/projects/156
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Organisms: No Organisms specified
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Project created: 29th Jul 2019
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Projects: Simulation Foundries
Institutions: University of Stuttgart
https://orcid.org/0000-0001-8809-1856
Polyglot European Scientist. I thrive working in interdisciplinary environments combining the study of enzyme reactions and mechanisms with bioinformatics, molecular modelling, automated data analysis and data stewardship.
Projects: Simulation Foundries
Institutions: University of Stuttgart
Determination of thermophysical properties (densities, diffusion coefficients, energy contributions) of different methanol-water mixtures using molecular dynamics simulations.
Submitter: Gudrun Gygli
Investigation: 1 hidden item
Assays: Analysis Version 1.5, Preparation, Results, Simulation Version 1.5
Preparation needed to use Simulation Foundry, Version 1.5.
Please read the manual before working with this Simulation Foundry.
Pay careful attention to the installation instructions.
Note the known issues.
Submitter: Gudrun Gygli
Assay type: Instructions
Technology type: Technical Computer Installation
Investigation: 1 hidden item
This is the simulation part of the Simulation Foundry, Version 1.5.
Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.
Make sure you followed the instructions in "Preparation" before running this.
Submitter: Gudrun Gygli
Assay type: Molecular Dynamics
Technology type: All-Atom
Investigation: 1 hidden item
This is the analysis part of the Simulation Foundry, Version 1.5.
Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.
Make sure you followed the instructions in "Preparation" before running this.
Submitter: Gudrun Gygli
Biological problem addressed: various analyses of molecular dynamics simulations
Investigation: 1 hidden item
Here would be the results from the Analysis part of the Simulation foundry. For the newest version, which was improved based on reviewers comments to represent best practices, of the Simulation Foundry for Methanol-Water mixtures no such results exist yet.
Submitter: Gudrun Gygli
Biological problem addressed: various analyses of molecular dynamics simulations
Investigation: 1 hidden item
Follow the instructions in this file to get the necessary software packages to run the Simulation Foundry Version 1.5.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Download
Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Abstract (Expand)
Authors: Gudrun Gygli, Juergen Pleiss
Date Published: 27th Apr 2020
Publication Type: Journal
Scripts and Input Files for Simulation V1.5
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Overview of the results obtained from the Simulation Foundry.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Overview of the quality control checks obtained from the Simulation Foundry.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
This is a list of errors that can be produced if the Simulation Foundry is not used correctly - the messages are cryptic, hopefully the file is helpful to some.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Manual to Simulation Foundry Version 1.5.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Scripts and Input Files for Analysis V1.5
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
OPLSAA force field used by GROMACS on the BINAC Supercomputer (chem/gromacs/5.1.4-gnu-4.9, https://wiki.bwhpc.de/e/Category:BwForCluster_BinAC )
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Screenshot of the directory structure required for the Simulation Foundry.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
